Törönen P - Search Results

1

Global analysis of aging-related protein structural changes uncovers enzyme-polymerization-based control of longevity.

Paukštytė J, López Cabezas RM, Feng Y, Tong K, Schnyder D, Elomaa E, Gregorova P, Doudin M, Särkkä M, Sarameri J, Lippi A, Vihinen H, Juutila J, Nieminen A, Törönen P, Holm L, Jokitalo E, Krisko A, Huiskonen J, Sarin LP, Hietakangas V, Picotti P, Barral Y, Saarikangas J. Paukštytė J, et al. Among authors: toronen p. Mol Cell. 2023 Sep 21;83(18):3360-3376.e11. doi: 10.1016/j.molcel.2023.08.015. Epub 2023 Sep 11. Mol Cell. 2023. PMID: 37699397 Free article.

2

Bayesian search of functionally divergent protein subgroups and their function specific residues.

Marttinen P, Corander J, Törönen P, Holm L. Marttinen P, et al. Among authors: toronen p. Bioinformatics. 2006 Oct 15;22(20):2466-74. doi: 10.1093/bioinformatics/btl411. Epub 2006 Jul 26. Bioinformatics. 2006. PMID: 16870932

3

Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana.

Kankainen M, Brader G, Törönen P, Palva ET, Holm L. Kankainen M, et al. Among authors: toronen p. Nucleic Acids Res. 2006;34(18):e124. doi: 10.1093/nar/gkl694. Epub 2006 Sep 26. Nucleic Acids Res. 2006. PMID: 17003050 Free PMC article.

4

Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function.

Törönen P, Ojala PJ, Marttinen P, Holm L. Törönen P, et al. BMC Bioinformatics. 2009 Sep 23;10:307. doi: 10.1186/1471-2105-10-307. BMC Bioinformatics. 2009. PMID: 19775443 Free PMC article.

5

Generation of Gene Ontology benchmark datasets with various types of positive signal.

Törönen P, Pehkonen P, Holm L. Törönen P, et al. BMC Bioinformatics. 2009 Oct 7;10:319. doi: 10.1186/1471-2105-10-319. BMC Bioinformatics. 2009. PMID: 19811632 Free PMC article.

6

GOParGenPy: a high throughput method to generate gene ontology data matrices.

Kumar AA, Holm L, Toronen P. Kumar AA, et al. Among authors: toronen p. BMC Bioinformatics. 2013 Aug 8;14:242. doi: 10.1186/1471-2105-14-242. BMC Bioinformatics. 2013. PMID: 23927037 Free PMC article.

7

Gene set analysis: limitations in popular existing methods and proposed improvements.

Mishra P, Törönen P, Leino Y, Holm L. Mishra P, et al. Among authors: toronen p. Bioinformatics. 2014 Oct;30(19):2747-56. doi: 10.1093/bioinformatics/btu374. Epub 2014 Jun 5. Bioinformatics. 2014. PMID: 24903419

8

PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment.

Koskinen P, Törönen P, Nokso-Koivisto J, Holm L. Koskinen P, et al. Among authors: toronen p. Bioinformatics. 2015 May 15;31(10):1544-52. doi: 10.1093/bioinformatics/btu851. Epub 2015 Jan 8. Bioinformatics. 2015. PMID: 25653249

9

Robust multi-group gene set analysis with few replicates.

Mishra PP, Medlar A, Holm L, Törönen P. Mishra PP, et al. Among authors: toronen p. BMC Bioinformatics. 2016 Dec 9;17(1):526. doi: 10.1186/s12859-016-1403-0. BMC Bioinformatics. 2016. PMID: 27938331 Free PMC article.

10

PANNZER2: a rapid functional annotation web server.

Törönen P, Medlar A, Holm L. Törönen P, et al. Nucleic Acids Res. 2018 Jul 2;46(W1):W84-W88. doi: 10.1093/nar/gky350. Nucleic Acids Res. 2018. PMID: 29741643 Free PMC article.

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